rs11833537

chr12-4170941-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.336 in 152,092 control chromosomes in the GnomAD database, including 9,260 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (9260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51080 AN: 151972 Hom.: 9259 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.323

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.336 AC: 51094 AN: 152092 Hom.: 9260 Cov.: 32 AF XY: 0.334 AC XY: 24856 AN XY: 74338

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.320

Alfa AF: 0.388 Hom.: 20355

Bravo AF: 0.317

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.0
Dann	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11833537; hg19: chr12-4280107;